Bidirectional epigenetic editing reveals hierarchies in gene regulation

Nature Biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: May 17, 2024

Abstract CRISPR perturbation methods are limited in their ability to study non-coding elements and genetic interactions. In this study, we developed a system for bidirectional epigenetic editing, called CRISPRai, which apply activating (CRISPRa) repressive (CRISPRi) perturbations two loci simultaneously the same cell. We CRISPRai Perturb-seq by coupling dual gRNA detection with single-cell RNA sequencing, enabling of pooled mixed population. applied platform interaction between hematopoietic lineage transcription factors, SPI1 GATA1, discovered novel characteristics co-regulation on downstream target genes, including differences GATA1 occupancy at genes that regulated through different modes. also studied regulatory landscape IL2 (interleukin-2) Jurkat T cells, primary cells chimeric antigen receptor (CAR) elucidated mechanisms enhancer-mediated gene regulation. facilitates investigation context-specific interactions, provides new insights into regulation will enable exploration disease-associated variants.

Language: Английский

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The functional role of CST1 and CCL26 in asthma development

Immunity Inflammation and Disease, Journal Year: 2024, Volume and Issue: 12(1)

Published: Jan. 1, 2024

Abstract Background Asthma is the most common chronic disease in children with an increasing prevalence. Its development caused by genetic and environmental factors allergic sensitization a known trigger. Dog allergens affect up to 30% of all dog dander‐sensitized show increased expression cystatin‐1 ( CST1 ) eotaxin‐3 CCL26 nasal epithelium. The aim our study was investigate functional mechanism alveolar basal epithelial cell line A549. Methods A549 cells were transfected individual overexpression vectors for RNA sequencing performed examine transcriptomics. edgeR used identify differentially expressed genes (= DEG, |log 2 FC | ≥ 2, FDR < 0.01). protein levels overexpressing analyzed using Target 96 inflammation panel from OLINK (antibody‐mediated proximity extension–based assay; Proteomics). Differentially proteins considered FC| 1, p .05. Results resulted total 27 DEG (1 upregulated 26 downregulated) 137 (0 downregulated). gene ontology enrichment analysis showed significant downregulation type I III interferon signaling pathway as well interferon‐stimulated genes. At level, induced significantly CCL3, whereas led HGF, decrease CXCL11, CCL20, CCL3 CXCL10. Conclusion Our results indicate that cause related inflammatory proteins. It might higher susceptibility, mainly asthma, agonist CCR‐3‐carrying cells, such eosinophils Th2 lymphocytes, mostly active asthma.

Language: Английский

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IFITM3 variants point to a critical role in emergent virus infections

mBio, Journal Year: 2025, Volume and Issue: unknown

Published: April 16, 2025

ABSTRACT Interferon-induced transmembrane protein 3 (IFITM3) is a cellular that restricts numerous viral infections by blocking virus–host membrane fusion. In humans, there are two IFITM3 single nucleotide polymorphisms (SNPs), rs12252-C and rs34481144-A, decrease activity have been associated with severe illness following influenza virus infections. Mice lacking show increased severity, supporting this association. However, some studies do not find consistent link between SNPs infection causing uncertainty about its role in vivo . Review of the literature indicates primarily disease emergent viruses, such as 2009 H1N1 pandemic zoonotic H7N9 virus. Similarly, reported to be risk factors for severity other infections, including SARS-CoV-2, Hantaan virus, HIV. contrast, most failed an association examined seasonal influenza. We posit adaptive immune mechanisms, pre-existing antibodies memory T cells against seasonally circulating compensate deficiencies, therefore masking propose critical defending viruses should key focus public health strategies prevent emergence spread novel pathogens, individuals carrying potentially benefiting from broadened vaccine coverage, avoidance animal reservoirs, or enhanced protect themselves wider population.

Language: Английский

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Altered platelet-megakaryocyte endocytosis and trafficking of albumin and fibrinogen in RUNX1 haplodeficiency

Blood Advances, Journal Year: 2024, Volume and Issue: 8(7), P. 1699 - 1714

Published: Feb. 8, 2024

Abstract Platelet α-granules have numerous proteins, some synthesized by megakaryocytes (MK) and others not but incorporated endocytosis, an incompletely understood process in platelets/MK. Germ line RUNX1 haplodeficiency, referred to as familial platelet defect with predisposition myeloid malignancies (FPDMMs), is associated thrombocytopenia, dysfunction, granule deficiencies. In previous studies, we found that albumin, fibrinogen, immunoglobulin G (IgG) were decreased a patient FPDMM. We now show endocytosis of fluorescent-labeled IgG the his daughter megakaryocytic human erythroleukemia (HEL) cells, small interfering RNA knockdown (KD) increased uptake these proteins over 24 hours compared control increases caveolin-1 flotillin-1 (2 independent regulators clathrin-independent endocytosis), LAMP2 (a lysosomal marker), RAB11 marker recycling endosomes), IFITM3. Caveolin-1 downregulation RUNX1-deficient HEL cells abrogated fibrinogen. Albumin, partially colocalized caveolin-1. KD resulted colocalization albumin flotillin fibrinogen RAB11, suggesting altered trafficking both proteins. The well levels caveolin-1, flotillin-1, LAMP2, IFITM3, recapitulated short hairpin CD34+-derived MK. To our knowledge, studies provide first evidence impaired patients RUNX1-haplodeficiency suggest enhanced defective trafficking, leading loss distinct mechanisms. This study provides new insights into mechanisms governing α-granule deficiencies RUNX1-haplodeficiency.

Language: Английский

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Interferon-stimulated genes and their antiviral activity against SARS-CoV-2

mBio, Journal Year: 2024, Volume and Issue: 15(9)

Published: Aug. 22, 2024

ABSTRACT The coronavirus disease 2019 (COVID-19) pandemic remains an international health problem caused by the recent emergence of severe acute respiratory syndrome 2 (SARS-CoV-2). As May 2024, SARS-CoV-2 has more than 775 million cases and over 7 deaths globally. Despite current vaccination programs, infections are still rapidly increasing, mainly due to appearance spread new variants, variations in immunization rates, limitations vaccines preventing transmission. This underscores need for pan-variant antivirals treatments. interferon (IFN) system is a critical element innate immune response serves as frontline defense against viruses. It induces generalized antiviral state transiently upregulating hundreds IFN-stimulated genes (ISGs). To gain deeper comprehension SARS-CoV-2, its connection COVID-19 pathogenesis, potential therapeutic implications, this review provides detailed overview fundamental aspects diverse ISGs identified their properties SARS-CoV-2. emphasizes importance these proteins controlling viral replication spread. Furthermore, we explore methodological approaches identification conduct comparative analysis with other Deciphering roles interactions pathogens can help identify novel targets therapies enhance our preparedness confront future threats.

Language: Английский

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Low-dose-rate ionizing radiation affects innate immunity protein IFITM3 in a mouse model of Alzheimer’s disease

International Journal of Radiation Biology, Journal Year: 2023, Volume and Issue: 99(11), P. 1649 - 1659

Published: May 11, 2023

Purpose Although the adverse health risks associated with low-dose radiation (LDR) are highly debated, relevant data on neuronal function following chronic LDR exposure still lacking.Materials and Methods To confirm effect of progression Alzheimer's disease (AD), we investigated changes in behavior neuroinflammation after wild-type (WT) 5xFAD (TG) mice, an animal model AD. WT TG classified by genotyping, were exposed to low-dose-rate for 112 days, cumulative doses 0, 0.1, 0.3 Gy, then evaluated using open-field Y-maze behavioral tests. Changes levels APP processing- neuroinflammation-related genes also investigated.Results No apparent change was evident either non-spatial memory or locomotor activity, as examined open field tests, respectively. did not affect processing, gliosis (Iba1 GFAP), inflammatory cytokines (IL-1b, IL-6, TNF-a), IFN-γ significantly downregulated mice exposure. In additional analysis, related IFN signaling found that interferon induced transmembrane protein 3 (IFITM3) decreased 0.1 Gy.Conclusions Therefore, this study revealed possibility could AD, which may be IFN-related signaling, especially IFITM3. Our findings suggest further studies required regarding potential role

Language: Английский

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Tumor-specific activation of folate receptor beta enables reprogramming of immune cells in the tumor microenvironment

Frontiers in Immunology, Journal Year: 2024, Volume and Issue: 15

Published: Feb. 7, 2024

Folate receptors can perform folate transport, cell adhesion, and/or transcription factor functions. The beta isoform of the receptor (FRβ) has attracted considerable attention as a biomarker for immunosuppressive macrophages and myeloid-derived suppressor cells, however, its role in immunosuppression remains uncharacterized. We demonstrate here that FRβ cannot bind on healthy tissue macrophages, but does after macrophage incubation anti-inflammatory cytokines or cancer cell-conditioned media. further show becomes functionally active following infiltration into solid tumors, we exploit this tumor-induced activation to target toll-like 7 agonist specifically myeloid cells tumors without altering tissues. then use single-cell RNA-seq characterize changes gene expression induced by targeted repolarization tumor-associated finally their not only own phenotype, also induces proinflammatory shift all other immune same tumor mass, leading potent suppression growth. Because selective reprogramming is accompanied no systemic toxicity, propose it should constitute safe method reprogram microenvironment.

Language: Английский

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The Antiviral Activity of Interferon-Induced Transmembrane Proteins and Virus Evasion Strategies

Viruses, Journal Year: 2024, Volume and Issue: 16(5), P. 734 - 734

Published: May 6, 2024

Interferons (IFNs) are antiviral cytokines that defend against viral infections by inducing the expression of interferon-stimulated genes (ISGs). Interferon-inducible transmembrane proteins (IFITMs) 1, 2, and 3 crucial ISG products members CD225 protein family. Compelling evidence shows IFITMs restrict infection many unrelated viruses inhibiting virus–cell membrane fusion at virus entry step via modulation lipid composition properties. Meanwhile, can evade IFITMs’ restrictions either directly interacting with glycoproteins or altering native pathway. At same time, cumulative suggests context-dependent multifaceted roles in modulating cell signaling. Here, we review diverse mechanisms IFITMs, antagonizing strategies, regulation IFITM activity host cells. The behind could aid development broad-spectrum antivirals enhance preparedness for future pandemics.

Language: Английский

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Bioinformatic analysis and identification of macrophage polarization-related genes in intervertebral disc degeneration

American Journal of Translational Research, Journal Year: 2024, Volume and Issue: 16(5), P. 1891 - 1906

Published: Jan. 1, 2024

The relationship between macrophage polarization-related genes (MPRGs) and intervertebral disc degeneration (IDD) is unclear. purpose of this study was to identify biomarkers associated with IDD.

Language: Английский

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The ‘dispanins’ and related proteins in physiology and neurological disease

Trends in Neurosciences, Journal Year: 2024, Volume and Issue: 47(8), P. 622 - 634

Published: July 17, 2024

Language: Английский

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